Taxonomy is a system of classification used mainly in the biological sciences to describe and categorize life. Life evolves and so in designing a SharePoint taxonomy it is wise to design a system or a set of principles for your information architecture that reflects this simple reality of all life, including business. It changes. SharePoint has its own internal structure. Here is the basic hierarchical view:

• Server Farms, with different servers with different roles.
• Web Applications for defining how users will access the content, such as via an Extranet.
• Site Collections which are the main grouping of content and user access groups.
• Sites and subsites are what site collections consist of in one site collection they can share templates, web parts and users easily.
• Web Part pages, Web Part zones and Web Parts these are the way SharePoint is displayed via the web browser.
• Lists and Libraries. These are where content is stored.
• Content Types, Properties and Views. These are the way metadata is stored around content and give it structure.
• Applications such as KPIs and Workflows can also be added to better map business process to SharePoint.

All of these elements are the skeleton on which you will hang the content your users produce. My recommendation is to think of the Site Collection as your starting point for where to put data. This gives you the flexibility to expand down into subsites, but also across into multiple site collections. A site collection could be thought of as the equivalent of a file share. It will most likely have a clearly defined audience. The audience helps you group content, it also helps you assign an administrator for the content. In SharePoint, like in Windows Shares, users have the ability to create their own structure. This gives them freedom, but it can also lead to poor structure and information being difficult to find by those not familiar with the structure. Initially grouping data into site collections will give you an initial structure for your content. These can be assigned to departments or teams in you rorganization.

The next most important aspect in your taxonomy is the structure within your site collections. This can be kept consistent by creating content types. These are a group of properties for a category of content such as a proposal, presentation or invoice. Allowing users to select which content type gives them freedom but it also structures the data to keep it available through search for the organization as a whole.

Site templates and within them list templates and views can also be used to give users something to build their content with, but also ensure there is a structure.

Products like Echo for SharePoint allow you to replicate changes to your template elements across site collections to ensure they keep up to date with your changing taxonomy so you can always have an up to date taxonomy for your organization.